Taxonomic distribution of proteins containing YaeQ domains

The tree below includes only several representative species and genera. The complete taxonomic breakdown of all proteins containing YaeQ domains can be accessed here. Click the counts or percentage values to display the corresponding proteins.

Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterasesuperfamily.

Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K
Nucleic Acids Res. 2012; 40: 7016-45

Proteins belonging to PD-(D/E)XK phosphodiesterases constitute a functionallydiverse superfamily with representatives involved in replication, restriction,DNA repair and tRNA-intron splicing. Their malfunction in humans triggers severe diseases, such as Fanconi anemia and Xeroderma pigmentosum. To date there havebeen several attempts to identify and classify new PD-(D/E)KK phosphodiesterases using remote homology detection methods. Such efforts are complicated, becausethe superfamily exhibits extreme sequence and structural divergence. Usingadvanced homology detection methods supported with superfamily-wide domainarchitecture and horizontal gene transfer analyses, we provide a comprehensivereclassification of proteins containing a PD-(D/E)XK domain. The PD-(D/E)XKphosphodiesterases span over 21,900 proteins, which can be classified into 121groups of various families. Eleven of them, including DUF4420, DUF3883, DUF4263, COG5482, COG1395, Tsp45I, HaeII, Eco47II, ScaI, HpaII and Replic_Relax, are newlyassigned to the PD-(D/E)XK superfamily. Some groups of PD-(D/E)XK proteins arepresent in all domains of life, whereas others occur within small numbers oforganisms. We observed multiple horizontal gene transfers even between humanpathogenic bacteria or from Prokaryota to Eukaryota. Uncommon domain arrangementsgreatly elaborate the PD-(D/E)XK world. These include domain architecturessuggesting regulatory roles in Eukaryotes, like stress sensing and cell-cycleregulation. Our results may inspire further experimental studies aimed atidentification of exact biological functions, specific substrates and molecularmechanisms of reactions performed by these highly diverse proteins.

A gene, yaeQ, that suppresses reduced operon expression caused by mutations inthe transcription elongation gene rfaH in Escherichia coli and Salmonellatyphimurium.

Wong KR, Hughes C, Koronakis V
Mol Gen Genet. 1998; 257: 693-6

RfaH is a specialised transcription elongation protein. We isolated from aSalmonella typhimurium rfaH suppressor strain a gene that complements in transthe attenuated transcription of the hlyCABD hemolysin operon caused by an rfaHmutation. The gene is homologous to the uncharacterised Escherichia coli geneyaeQ. YaeQ did not increase hlyCABD-encoded hemolysin activity in the RfaH+ wild type, nor did it increase the level of RfaH protein. YaeQ also complements arfaH::Tn5 null mutation, indicating that it compensates for loss of RfaH functionwithout interaction between the two proteins.